Abstract

Background

Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively
little is known about its genome. The availability of a genome-wide physical map allows
rapid fine mapping of QTL, development of high-density genome maps, and sequencing
of the entire genome. However, no such a physical map has been developed in chickpea.

Results

We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint
analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in
this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7
×) of the fingerprints validated and used in the physical map assembly. The physical
map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones
and having an average physical length of 559 kb. The contigs collectively span approximately
1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing
or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical
map and confirming its utility in fine mapping and cloning of QTL.

Conclusion

The physical map represents the first genome-wide, BAC/BIBAC-based physical map of
chickpea. This map, along with other genomic resources previously developed in the
species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research
in chickpea and other legume species. The inclusion of transformation-ready BIBACs
in the map greatly facilitates its utility in functional analysis of the legume genomes.